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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ggtreeSpace.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ggtreeSpace_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ggtreeSpace.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggtreeSpace/DESCRIPTION’ ... OK
* this is package ‘ggtreeSpace’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ggtreeSpace’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
intern_call: no visible binding for global variable ‘dat’
Undefined global functions or variables:
  dat
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'geom_treespace.Rd':
geom_treespace
  Code: function(tr, trait, mapping = NULL, ...)
  Docs: function(tr, data, mapping = NULL, ...)
  Argument names in code not in docs:
    trait
  Argument names in docs not in code:
    data
  Mismatches in argument names:
    Position: 2 Code: trait Docs: data

Codoc mismatches from Rd file 'ggtreespace.Rd':
ggtreespace
  Code: function(tr, trait, mapping = NULL, ...)
  Docs: function(tr, data, mapping = NULL, ...)
  Argument names in code not in docs:
    trait
  Argument names in docs not in code:
    data
  Mismatches in argument names:
    Position: 2 Code: trait Docs: data

Codoc mismatches from Rd file 'make_ts_data.Rd':
make_ts_data
  Code: function(tr, trait)
  Docs: function(tr, data)
  Argument names in code not in docs:
    trait
  Argument names in docs not in code:
    data
  Mismatches in argument names:
    Position: 2 Code: trait Docs: data

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/ggtreeSpace.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ggtreeSpace
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘ggtreeSpace’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ggtreeSpace)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(ggtreeSpace)
> 
> test_check("ggtreeSpace")
ggtree v3.14.0 Learn more at https://yulab-smu.top/contribution-tree-data/

Please cite:

Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan
Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu. Ggtree: A serialized data
object for visualization of a phylogenetic tree and annotation data.
iMeta 2022, 1(4):e56. doi:10.1002/imt2.56
Loading required package: ape

Attaching package: 'ape'

The following object is masked from 'package:ggtree':

    rotate

Loading required package: maps

Attaching package: 'dplyr'

The following object is masked from 'package:ape':

    where

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Joining with `by = join_by(node)`
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 4 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  1.076   0.067   1.140